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Fishes

Fishes is an international, peer-reviewed, scientific, open access journal covering fishes and aquatic animals research, and is published monthly online by MDPI.
The Iberian Society of Ichthyology (SIBIC) and Brazilian Society of Aquaculture and Aquatic Biology (Aquabio) are affiliated with Fishes and their members receive a discount on the article processing charges.
Quartile Ranking JCR - Q1 (Marine and Freshwater Biology)

All Articles (2,553)

Early detection and effective monitoring of aquatic environments are essential for detecting and mitigating potential ecological threats to aquatic organisms and for ensuring the sustainable management of freshwater ecosystems. Passive sampling is an emerging approach for environmental DNA (eDNA) collection in aquatic systems while active sampling involves controlled collection and filtration of water. This study evaluates active and passive sampling methods in a riverine system for detecting eDNA from Atlantic salmon (Salmo salar) and its lethal ectoparasite Gyrodactylus salaris. Sampling was conducted in the Sande River, Vestfold County, Norway. The loop-mediated isothermal amplification (LAMP) method was employed due to its high efficiency and specificity for amplifying target genes. The selected genetic markers were mitochondrial cytochrome B (Cyt B) DNA for S. salar and cytochrome c oxidase 1 (COX1) for G. salaris. The results indicate that host eDNA was readily detected using both sampling methods, whereas detection of G. salaris was more effective using active sampling. These findings provide valuable insight into optimizing eDNA detection protocols for both host and parasite, demonstrating specificity and sensitivity of LAMP in detecting the target organisms. This case study contributes to the development of conservation strategies aimed at preserving Atlantic salmon populations and freshwater biodiversity.

7 February 2026

Illustration of eDNA sampling techniques employed in Sande River in this study.

To evaluate the potential of compound attractants in ameliorating diet-induced intestinal dysfunction in Siniperca chuatsi fed commercial compound feed, this study investigated their effects on intestinal metabolism and microbiota composition. In this study, four distinct diets are formulated: a control diet without attractants and three experimental diets supplemented with compound attractants A (nucleotides and L-glutamic acid), B (nucleotides, L-glutamic acid, and allicin), and C (nucleotides, L-glutamic acid, and betaine). Over a period of 8 weeks, groups of S. chuatsi were fed these diets, after which we assessed the intestinal microbiota and transcriptomic responses. KEGG pathway analysis of differentially expressed genes (DEGs) indicated that the A group exhibited significant changes predominantly in intestinal cholesterol homeostasis and inflammatory responses. The B group showed DEGs primarily associated with mucosal immune functions and pro-inflammatory cytokine signaling. Diversely, the C group revealed DEGs chiefly tied to immune and inflammatory response pathways. Furthermore, the intestinal microbiota exhibited beneficial modifications at both the phylum and genus levels in the A and B groups, while such beneficial shifts were not observed in the C group. These findings indicated that dietary supplementation with compound attractants A and B could positively influence both the intestinal transcriptomic landscape and microbiota composition in S. chuatsi, highlighting their potential as effective additives in compound feeds for aquaculture.

7 February 2026

Summary of the differential analyses results of RNA-seq data. (A) The principal component analyses (PCA) of the intestinal transcriptome. (B) Volcano plot of DEGs in AGT vs. ConGT. (C) Volcano plot of DEGs in BGT vs. ConGT. (D) Volcano plot of DEGs in CGT vs. ConGT. Black dots represent genes showing no significant differences in expression. Red and green dots represent significantly up-regulated and down-regulated DEGs, respectively.

To assess the status of Coilia nasus resources in the Yangtze River Estuary and support evaluation of fishing ban effectiveness, this study integrated fishery resource survey data and environmental variables collected from 2023 to 2025. A generalized additive model (GAM) was applied to examine post-ban recovery patterns of C. nasus and the environmental drivers shaping its spatiotemporal distribution. The results revealed pronounced seasonal variation in biomass, with autumn (November) values significantly higher than those in spring and summer. Biomass peaked in autumn 2024, forming a persistent and highly concentrated aggregation. Spatial analyses further indicated that high-biomass areas were consistently distributed within the brackish-water mixing zone of the outer estuary, corresponding to migratory pathways and foraging requirements of the species. GAM results demonstrated that the spatiotemporal distribution of C. nasus was jointly regulated by multiple environmental factors. In spring, temperature, depth, transparency, pH, dissolved oxygen (DO), and chlorophyll-a (Chl-a) exerted significant effects; in summer, salinity and pH were the dominant drivers; and in autumn, temperature, pH, salinity, DO, ammonium (NH4+–N), nitrate (NO3–N), and phosphate (PO43−–P) showed significant influences. This study provides scientific evidence to support the management of C. nasus resources, particularly in the brackish-water mixing zone of the outer Yangtze River Estuary, and to improve evaluation of fishing-ban effectiveness.

6 February 2026

Sampling points of C. nasus in the Yangtze River Estuary, China.

IMTA Production of Pacific White Shrimp Integrated with Mullet, Sea Cucumber, Oyster, and Salicornia in a Biofloc System

  • Enrique A. Estévez Hernández,
  • Ivanilson Santos and
  • Luís H. Poersch
  • + 8 authors

Integrated multitrophic aquaculture (IMTA) emerges as a sustainable strategy to control the excess of solids and inorganic nutrients that tend to increase in the biofloc system (BFT) cycle, since the model integrates organisms from different trophic levels sharing the same system and nutrients. Thus, this study compared a Penaeus vannamei monoculture system with an integrated biofloc system including Mugil liza, Holothuria grisea, Crassostrea tulipa, and Salicornia neei, focusing on water quality and the performance of organisms and systems. This study consisted of three monoculture systems (16 m3; 375 shrimp m−3) and three IMTA systems, composed of a shrimp tank (16 m3), a mullet tank (4 m3; 30 ind m−3), a combined tank (3 m3) for oysters (45 ind m−3) and sea cucumbers (3 ind m−2), and a Salicornia neei bed (2.78 m2; 37 ind m−2). All IMTA systems operated in recirculation without water exchange, using 10% of the established biofloc inoculum. The IMTA system had half the hydrated lime use (2.13 vs. 4.29 kg), lower solids (299.56 vs. 373.33 mg L−1), and reduced sludge production (9.37 vs. 15.87 kg). Shrimp growth was similar in both systems. Mullet grew adequately with a survival rate of 95.8%, but oysters showed a survival rate of 45.7%. Sea cucumber had a survival rate of 100% until day 28, when a marked decline appeared, strongly correlated with rising temperature (>28 °C; r = −0.71). This resulted in a significant increase in solids in the last weeks, suggesting that the population decline reduces solids control capacity. Furthermore, the biofloc in IMTA was dominated by coccoid forms, with lower proportions of filamentous and cyanobacterial forms.

5 February 2026

Illustrative representation of the IMTA system. Compartment 1: Shrimp tank; Compartment 2: Mullet tank; Compartment 3: Oyster and Sea cucumber tank; and Compartment 4: Salicornia hydroponic bench.

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Fishes - ISSN 2410-3888